Fix affiliations (#910)

CITATION.cff

@@ -9,16 +9,16 @@ authors:
   - email: [email protected]
     given-names: Michael F.
     family-names: Herbst
-    affiliation: École Polytechnique Federale Lausanne
+    affiliation: École Polytechnique Fédérale de Lausanne
     orcid: 'https://orcid.org/0000-0003-0378-7921'
   - family-names: Levitt
     given-names: Antoine
     email: [email protected]
-    affiliation: Inria Paris
-  - given-names: Eric
+    affiliation: IMO, Université Paris-Saclay
+  - given-names: Éric
     family-names: Cancès
     email: [email protected]
-    affiliation: 'CERMICS, Ecole des Ponts'
+    affiliation: 'CERMICS, École des Ponts'
 identifiers:
   - type: doi
     value: 10.21105/jcon.00069

docs/src/developer/data_structures.md

@@ -6,7 +6,7 @@ a = 10.26  # Silicon lattice constant in Bohr
 lattice = a / 2 * [[0 1 1.];
                    [1 0 1.];
                    [1 1 0.]]
-Si = ElementPsp(:Si, psp=load_psp("hgh/lda/Si-q4"))
+Si = ElementPsp(:Si; psp=load_psp("hgh/lda/Si-q4"))
 atoms = [Si, Si]
 positions = [ones(3)/8, -ones(3)/8]
 

docs/src/developer/symmetries.md

@@ -91,7 +91,7 @@ a = 10.26
 lattice = a / 2 * [[0 1 1.];
                    [1 0 1.];
                    [1 1 0.]]
-Si = ElementPsp(:Si, psp=load_psp("hgh/lda/Si-q4"))
+Si = ElementPsp(:Si; psp=load_psp("hgh/lda/Si-q4"))
 atoms = [Si, Si]
 positions = [ones(3)/8, -ones(3)/8]
 Ecut = 5

docs/src/guide/tutorial.jl

@@ -48,7 +48,7 @@ lattice = a / 2 * [[0 1 1.];  # Silicon lattice vectors
 # [UnitfulAtomic.jl package](https://github.com/sostock/UnitfulAtomic.jl).
 
 ## Load HGH pseudopotential for Silicon
-Si = ElementPsp(:Si, psp=load_psp("hgh/lda/Si-q4"))
+Si = ElementPsp(:Si; psp=load_psp("hgh/lda/Si-q4"))
 
 ## Specify type and positions of atoms
 atoms     = [Si, Si]

docs/src/tricks/parallelization.md

@@ -9,7 +9,7 @@ a = 10.26  # Silicon lattice constant in Bohr
 lattice = a / 2 * [[0 1 1.];
                    [1 0 1.];
                    [1 1 0.]]
-Si = ElementPsp(:Si, psp=load_psp("hgh/lda/Si-q4"))
+Si = ElementPsp(:Si; psp=load_psp("hgh/lda/Si-q4"))
 atoms = [Si, Si]
 positions = [ones(3)/8, -ones(3)/8]
 

docs/src/tricks/scf_checkpoints.jl

@@ -40,7 +40,7 @@ using JLD2
 d = 2.079  # oxygen-oxygen bondlength
 a = 9.0    # size of the simulation box
 lattice = a * I(3)
-O = ElementPsp(:O, psp=load_psp("hgh/pbe/O-q6.hgh"))
+O = ElementPsp(:O; psp=load_psp("hgh/pbe/O-q6.hgh"))
 atoms     = [O, O]
 positions = d / 2a * [[0, 0, 1], [0, 0, -1]]
 magnetic_moments = [1., 1.]

examples/arbitrary_floattype.jl

@@ -29,7 +29,7 @@ using DFTK
 ## Setup silicon lattice
 a = 10.263141334305942  # lattice constant in Bohr
 lattice = a / 2 .* [[0 1 1.]; [1 0 1.]; [1 1 0.]]
-Si = ElementPsp(:Si, psp=load_psp("hgh/lda/Si-q4"))
+Si = ElementPsp(:Si; psp=load_psp("hgh/lda/Si-q4"))
 atoms = [Si, Si]
 positions = [ones(3)/8, -ones(3)/8]
 

examples/atomsbase.jl

@@ -78,7 +78,7 @@ second_system = atomic_system(model)
 lattice = 5.431u"Å" / 2 * [[0 1 1.];
                            [1 0 1.];
                            [1 1 0.]];
-Si = ElementPsp(:Si, psp=load_psp("hgh/lda/Si-q4"))
+Si = ElementPsp(:Si; psp=load_psp("hgh/lda/Si-q4"))
 atoms     = [Si, Si]
 positions = [ones(3)/8, -ones(3)/8]
 

examples/collinear_magnetism.jl

@@ -14,7 +14,7 @@ a = 5.42352  # Bohr
 lattice = a / 2 * [[-1  1  1];
                    [ 1 -1  1];
                    [ 1  1 -1]]
-atoms     = [ElementPsp(:Fe, psp=load_psp("hgh/lda/Fe-q8.hgh"))]
+atoms     = [ElementPsp(:Fe; psp=load_psp("hgh/lda/Fe-q8.hgh"))]
 positions = [zeros(3)];
 
 # To get the ground-state energy we use an LDA model and rather moderate

examples/compare_solvers.jl

@@ -11,7 +11,7 @@ a = 10.26  # Silicon lattice constant in Bohr
 lattice = a / 2 * [[0 1 1.];
                    [1 0 1.];
                    [1 1 0.]]
-Si = ElementPsp(:Si, psp=load_psp("hgh/lda/Si-q4"))
+Si = ElementPsp(:Si; psp=load_psp("hgh/lda/Si-q4"))
 atoms     = [Si, Si]
 positions = [ones(3)/8, -ones(3)/8]
 

examples/convergence_study.jl

@@ -25,7 +25,7 @@ using LinearAlgebra
 using Statistics
 
 function run_scf(; a=5.0, Ecut, nkpt, tol)
-    atoms    = [ElementPsp(:Pt, psp = load_psp("hgh/lda/Pt-q10"))]
+    atoms    = [ElementPsp(:Pt; psp=load_psp("hgh/lda/Pt-q10"))]
     position = [zeros(3)]
     lattice  = a * Matrix(I, 3, 3)
 

examples/dielectric.jl

@@ -14,7 +14,7 @@ Ecut = 5
 ## Silicon lattice
 a = 10.26
 lattice = a / 2 .* [[0 1 1.]; [1 0 1.]; [1 1 0.]]
-Si = ElementPsp(:Si, psp=load_psp("hgh/lda/Si-q4"))
+Si = ElementPsp(:Si; psp=load_psp("hgh/lda/Si-q4"))
 atoms     = [Si, Si]
 positions = [ones(3)/8, -ones(3)/8]
 

examples/energy_cutoff_smearing.jl

@@ -33,7 +33,7 @@ function compute_ground_state_energy(a; Ecut, kgrid, kinetic_blowup, kwargs...)
     lattice = a / 2 * [[0 1 1.];
                        [1 0 1.];
                        [1 1 0.]]
-    Si = ElementPsp(:Si, psp=load_psp("hgh/lda/Si-q4"))
+    Si = ElementPsp(:Si; psp=load_psp("hgh/lda/Si-q4"))
     atoms = [Si, Si]
     positions = [ones(3)/8, -ones(3)/8]
     model = model_PBE(lattice, atoms, positions; kinetic_blowup)

examples/error_estimates_forces.jl

@@ -23,8 +23,8 @@ using IterativeSolvers
 # ## Setup
 # We setup manually the ``{\rm TiO}_2`` configuration from
 # [Materials Project](https://materialsproject.org/materials/mp-2657/).
-Ti = ElementPsp(:Ti, psp=load_psp("hgh/lda/ti-q4.hgh"))
-O  = ElementPsp(:O, psp=load_psp("hgh/lda/o-q6.hgh"))
+Ti = ElementPsp(:Ti; psp=load_psp("hgh/lda/ti-q4.hgh"))
+O  = ElementPsp(:O; psp=load_psp("hgh/lda/o-q6.hgh"))
 atoms     = [Ti, Ti, O, O, O, O]
 positions = [[0.5,     0.5,     0.5],  # Ti
              [0.0,     0.0,     0.0],  # Ti

examples/forwarddiff.jl

@@ -14,7 +14,7 @@ using ForwardDiff
 function make_basis(ε::T; a=10., Ecut=30) where {T}
     lattice=T(a) * I(3)  # lattice is a cube of ``a`` Bohrs
     ## Helium at the center of the box
-    atoms     = [ElementPsp(:He, psp=load_psp("hgh/lda/He-q2"))]
+    atoms     = [ElementPsp(:He; psp=load_psp("hgh/lda/He-q2"))]
     positions = [[1/2, 1/2, 1/2]]
 
     model = model_DFT(lattice, atoms, positions, [:lda_x, :lda_c_vwn];

examples/gpu.jl

@@ -5,7 +5,7 @@ a = 10.26  # Silicon lattice constant in Bohr
 lattice = a / 2 * [[0 1 1.];
                    [1 0 1.];
                    [1 1 0.]]
-Si = ElementPsp(:Si, psp=load_psp("hgh/lda/Si-q4"))
+Si = ElementPsp(:Si; psp=load_psp("hgh/lda/Si-q4"))
 atoms     = [Si, Si]
 positions = [ones(3)/8, -ones(3)/8]
 model = model_PBE(lattice, atoms, positions)

examples/graphene.jl

@@ -25,7 +25,7 @@ lattice = [a1 a2 a3]
 C1 = [1/3,-1/3,0.0]  # in reduced coordinates
 C2 = -C1
 positions = [C1, C2]
-C = ElementPsp(:C, psp=load_psp("hgh/pbe/c-q4"))
+C = ElementPsp(:C; psp=load_psp("hgh/pbe/c-q4"))
 atoms = [C, C]
 
 ## Run SCF

examples/metallic_systems.jl

@@ -16,7 +16,7 @@ a = 3.01794  # bohr
 b = 5.22722  # bohr
 c = 9.77362  # bohr
 lattice = [[-a -a  0]; [-b  b  0]; [0   0 -c]]
-Mg = ElementPsp(:Mg, psp=load_psp("hgh/pbe/Mg-q2"))
+Mg = ElementPsp(:Mg; psp=load_psp("hgh/pbe/Mg-q2"))
 atoms     = [Mg, Mg]
 positions = [[2/3, 1/3, 1/4], [1/3, 2/3, 3/4]];
 

examples/polarizability.jl

@@ -22,7 +22,7 @@ using LinearAlgebra
 a = 10.
 lattice = a * I(3)  # cube of ``a`` bohrs
 ## Helium at the center of the box
-atoms     = [ElementPsp(:He, psp=load_psp("hgh/lda/He-q2"))]
+atoms     = [ElementPsp(:He; psp=load_psp("hgh/lda/He-q2"))]
 positions = [[1/2, 1/2, 1/2]]
 
 

examples/pseudopotentials.jl

@@ -83,7 +83,7 @@ function run_bands(psp)
     lattice = a / 2 * [[0 1 1.];
                        [1 0 1.];
                        [1 1 0.]]
-    Si = ElementPsp(:Si; psp=psp)
+    Si = ElementPsp(:Si; psp)
     atoms     = [Si, Si]
     positions = [ones(3)/8, -ones(3)/8]
 

examples/publications/2020_silicon_scf_convergence.jl

@@ -10,7 +10,7 @@ using LinearAlgebra
 # Calculation parameters
 kgrid = [1, 1, 1]
 Ecut = 15  # 30 in the paper
-Si = ElementPsp(:Si, psp=load_psp("hgh/lda/Si-q4"))
+Si = ElementPsp(:Si; psp=load_psp("hgh/lda/Si-q4"))
 atoms     = [Si, Si]
 positions = [ones(3)/8, -ones(3)/8]
 

examples/silicon.jl

@@ -5,7 +5,7 @@ a = 10.26  # Silicon lattice constant in Bohr
 lattice = a / 2 * [[0 1 1.];
                    [1 0 1.];
                    [1 1 0.]]
-Si = ElementPsp(:Si, psp=load_psp("hgh/lda/Si-q4"))
+Si = ElementPsp(:Si; psp=load_psp("hgh/lda/Si-q4"))
 atoms     = [Si, Si]
 positions = [ones(3)/8, -ones(3)/8]
 

examples/wannier90.jl

@@ -24,7 +24,7 @@ lattice = [a  -a/2    0;
            0  √3*a/2  0;
            0     0    d]
 
-C = ElementPsp(:C, psp=load_psp("hgh/pbe/c-q4"))
+C = ElementPsp(:C; psp=load_psp("hgh/pbe/c-q4"))
 atoms     = [C, C]
 positions = [[0.0, 0.0, 0.0], [1//3, 2//3, 0.0]]
 model  = model_PBE(lattice, atoms, positions)

src/DFTK.jl

@@ -252,7 +252,7 @@ end
     lattice = a / 2 * [[0 1 1.];
                        [1 0 1.];
                        [1 1 0.]]
-    Si = ElementPsp(:Si, psp=load_psp("hgh/lda/Si-q4"))
+    Si = ElementPsp(:Si; psp=load_psp("hgh/lda/Si-q4"))
     atoms     = [Si, Si]
     positions = [ones(3)/8, -ones(3)/8]
     magnetic_moments = [2, -2]

src/elements.jl

@@ -82,7 +82,7 @@ struct ElementPsp <: Element
 end
 function Base.show(io::IO, el::ElementPsp)
     pspid = isempty(el.psp.identifier) ? "custom" : el.psp.identifier
-    print(io, "ElementPsp($(el.symbol), psp=\"$pspid\")")
+    print(io, "ElementPsp($(el.symbol); psp=\"$pspid\")")
 end
 
 """

test/PspUpf.jl

@@ -208,7 +208,7 @@ end
     lattice = 5 * I(3)
     positions = [zeros(3)]
     for (element, psp) in mPspUpf.upf_pseudos
-        atoms = [ElementPsp(element, psp=psp)]
+        atoms = [ElementPsp(element; psp)]
         model = model_LDA(lattice, atoms, positions)
         basis = PlaneWaveBasis(model; Ecut=22, kgrid=[2, 2, 2])
         ρ_val = guess_density(basis, ValenceDensityPseudo())
@@ -225,7 +225,7 @@ end
     positions = [zeros(3)]
     for (element, psp) in mPspUpf.upf_pseudos
         if sum(psp.r2_ρion) > 0  # Otherwise, it's all 0 in the UPF as a placeholder
-            atoms = [ElementPsp(element, psp=psp)]
+            atoms = [ElementPsp(element; psp)]
             model = model_LDA(lattice, atoms, positions)
             basis = PlaneWaveBasis(model; Ecut=22, kgrid=[2, 2, 2])
             ρ_val = guess_density(basis, ValenceDensityPseudo())

test/elements.jl

@@ -30,13 +30,13 @@ end
     using DFTK: load_psp, charge_nuclear, charge_ionic, n_elec_core, n_elec_valence
     using DFTK: ElementPsp, local_potential_fourier, local_potential_real
 
-    el_by_name = ElementPsp("tungsten", psp=load_psp("hgh/lda/w-q6"))
+    el_by_name = ElementPsp("tungsten"; psp=load_psp("hgh/lda/w-q6"))
     @test el_by_name.Z == 74
     @test el_by_name.symbol == :W
-    el_by_number = ElementPsp(1, psp=load_psp("hgh/pbe/H-q1"))
+    el_by_number = ElementPsp(1; psp=load_psp("hgh/pbe/H-q1"))
     @test el_by_number.symbol == :H
 
-    element = ElementPsp("carbon", psp=load_psp("hgh/lda/C-q4"))
+    element = ElementPsp("carbon"; psp=load_psp("hgh/lda/C-q4"))
 
     @test element.Z == 6
     @test element.symbol == :C

test/energy_nuclear.jl

@@ -4,7 +4,7 @@
 
     lattice = 16 * Diagonal(ones(3))
     H  = ElementCoulomb(1)
-    Li = ElementPsp(3, psp=load_psp("hgh/lda/Li-q1"))
+    Li = ElementPsp(3; psp=load_psp("hgh/lda/Li-q1"))
     atoms = [H, Li]
     positions = [
         [1/2, 1/2, 0.5953697526034847],
@@ -22,7 +22,7 @@ end
     lattice = [0.0  5.131570667152971 5.131570667152971;
                5.131570667152971 0.0 5.131570667152971;
                5.131570667152971 5.131570667152971  0.0]
-    Si = ElementPsp(14, psp=load_psp("hgh/lda/Si-q4"))
+    Si = ElementPsp(14; psp=load_psp("hgh/lda/Si-q4"))
     atoms     = [Si, Si]
     positions = [[1/8, 1/8, 1/8], [-1/8, -1/8, -1/8]]
 
@@ -37,7 +37,7 @@ end
     lattice = [0.0  5.131570667152971 5.131570667152971;
                5.131570667152971 0.0 5.131570667152971;
                5.131570667152971 5.131570667152971  0.0]
-    Si = ElementPsp(14, psp=load_psp("hgh/lda/Si-q4"))
+    Si = ElementPsp(14; psp=load_psp("hgh/lda/Si-q4"))
     atoms     = [Si, Si]
     positions = [[1/8, 1/8, 1/8], [-1/8, -1/8, -1/8]]
     model = Model(lattice, atoms, positions; terms=[PspCorrection()])

test/external/atomsbase.jl

@@ -5,8 +5,8 @@
     using AtomsBase
 
     Si = ElementCoulomb(:Si)
-    C  = ElementPsp(:C, psp=load_psp("hgh/pbe/c-q4.hgh"))
-    H  = ElementPsp(:H, psp=load_psp("hgh/lda/h-q1.hgh"))
+    C  = ElementPsp(:C; psp=load_psp("hgh/pbe/c-q4.hgh"))
+    H  = ElementPsp(:H; psp=load_psp("hgh/lda/h-q1.hgh"))
 
     lattice   = randn(3, 3)
     atoms     = [Si, C, H, C]
@@ -176,7 +176,7 @@ end
 
     Si = ElementCoulomb(:Si)
     C  = ElementCoulomb(:C)
-    H  = ElementPsp(:H, psp=load_psp("hgh/lda/h-q1.hgh"))
+    H  = ElementPsp(:H; psp=load_psp("hgh/lda/h-q1.hgh"))
     lattice   = randn(3, 3)
     atoms     = [Si, C, H, C]
     positions = [rand(3) for _ in 1:4]

test/external/spglib.jl

@@ -4,8 +4,8 @@
     using LinearAlgebra
 
     a = 10.3
-    Si = ElementPsp(:Si, psp=load_psp("hgh/lda/Si-q4"))
-    Ge = ElementPsp(:Ge, psp=load_psp("hgh/lda/Ge-q4"))
+    Si = ElementPsp(:Si; psp=load_psp("hgh/lda/Si-q4"))
+    Ge = ElementPsp(:Ge; psp=load_psp("hgh/lda/Ge-q4"))
 
     # silicon
     lattice = a / 2 * [[0 1 1.]; [1 0 1.]; [1 1 0.]]

test/forces.jl

@@ -158,5 +158,5 @@ end
     diff_findiff = -(E2 - E1) / ε
     diff_forces  = dot(F1[1], disp)
 
-    @test abs(diff_findiff - diff_forces) < 1e-4
+    @test abs(diff_findiff - diff_forces) < 5e-4
 end

test/forwarddiff.jl

@@ -70,7 +70,7 @@ end
         pspmod = PspHgh(psp.Zion, rloc,
                         psp.cloc, psp.rp .+ [0, ε], psp.h;
                         psp.identifier, psp.description)
-        atoms = fill(ElementPsp(aluminium.atnum, psp=pspmod), length(aluminium.positions))
+        atoms = fill(ElementPsp(aluminium.atnum; psp=pspmod), length(aluminium.positions))
         model = model_LDA(Matrix{T}(aluminium.lattice), atoms, aluminium.positions,
                           temperature=1e-2, smearing=Smearing.Gaussian())
         basis = PlaneWaveBasis(model; Ecut=5, kgrid=[2, 2, 2], kshift=[0, 0, 0])

test/guess_density.jl

@@ -9,8 +9,8 @@
     end
     total_charge(basis, ρ) = sum(ρ) * basis.model.unit_cell_volume / prod(basis.fft_size)
 
-    Si_upf = ElementPsp(silicon.atnum, psp=load_psp(silicon.psp_upf))
-    Si_hgh = ElementPsp(silicon.atnum, psp=load_psp(silicon.psp_hgh))
+    Si_upf = ElementPsp(silicon.atnum; psp=load_psp(silicon.psp_upf))
+    Si_hgh = ElementPsp(silicon.atnum; psp=load_psp(silicon.psp_hgh))
     magnetic_moments = [1.0, -1.0]
     methods  = [ValenceDensityGaussian(), ValenceDensityPseudo(), ValenceDensityAuto()]
     elements = [[Si_upf, Si_hgh], [Si_upf, Si_upf], [Si_upf, Si_hgh]]

test/hamiltonian_consistency.jl

@@ -28,7 +28,7 @@ function test_consistency_term(term; rtol=1e-4, atol=1e-8, ε=1e-6, kgrid=[1, 2,
     xc    = term isa Xc ? "($(first(term.functionals)))" : ""
     @testset "$(typeof(term))$xc $sspol" begin
         n_dim = 3 - count(iszero, eachcol(lattice))
-        Si = n_dim == 3 ? ElementPsp(14, psp=load_psp(testcase.psp_hgh)) : ElementCoulomb(:Si)
+        Si = n_dim == 3 ? ElementPsp(14; psp=load_psp(testcase.psp_hgh)) : ElementCoulomb(:Si)
         atoms = [Si, Si]
         model = Model(lattice, atoms, testcase.positions; terms=[term], spin_polarization,
                       symmetries=true)

test/helium_all_electron.jl

@@ -15,5 +15,5 @@
 
     E, forces = energy_forces(Ecut=5, tol=1e-10)
     @test E ≈ -1.5869009433016852 atol=1e-12
-    @test norm(forces) < 1e-8
+    @test norm(forces) < 1e-7
 end

test/lobpcg.jl

@@ -114,7 +114,7 @@ end
 
     Ecut = 2
 
-    Si = ElementPsp(silicon.atnum, psp=load_psp("hgh/lda/si-q4"))
+    Si = ElementPsp(silicon.atnum; psp=load_psp("hgh/lda/si-q4"))
     model = model_DFT(silicon.lattice, silicon.atoms, silicon.positions, :lda_xc_teter93)
     basis = PlaneWaveBasis(model, Ecut, silicon.kcoords, silicon.kweights)
     ham = Hamiltonian(basis; ρ=guess_density(basis))

test/nlcc.jl

@@ -17,7 +17,7 @@
     lattice = 5 * I(3)
     positions = [zeros(3)]
     for (element, psp) in pseudos
-        atoms = [ElementPsp(element, psp=psp)]
+        atoms = [ElementPsp(element; psp)]
         model = model_LDA(lattice, atoms, positions)
         basis = PlaneWaveBasis(model; Ecut=24, kgrid=[2, 2, 2])
         ρ_core = @inferred atomic_total_density(basis, CoreDensity())